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WO2007014397A3 - Consecutive base single molecule sequencing - Google Patents

Consecutive base single molecule sequencing Download PDF

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Publication number
WO2007014397A3
WO2007014397A3 PCT/US2006/030245 US2006030245W WO2007014397A3 WO 2007014397 A3 WO2007014397 A3 WO 2007014397A3 US 2006030245 W US2006030245 W US 2006030245W WO 2007014397 A3 WO2007014397 A3 WO 2007014397A3
Authority
WO
WIPO (PCT)
Prior art keywords
single molecule
molecule sequencing
consecutive base
base single
sequencing
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2006/030245
Other languages
French (fr)
Other versions
WO2007014397A2 (en
Inventor
Timothy Harris
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Helicos BioSciences Corp
Original Assignee
Helicos BioSciences Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Helicos BioSciences Corp filed Critical Helicos BioSciences Corp
Priority to EP06800694A priority Critical patent/EP1907591A2/en
Priority to CA002616433A priority patent/CA2616433A1/en
Publication of WO2007014397A2 publication Critical patent/WO2007014397A2/en
Publication of WO2007014397A3 publication Critical patent/WO2007014397A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention provides methods for sequencing polynucleotide molecules using single molecule sequencing techniques, where a plurality of labeled nucleotides are incorporated consecutively into an individual primer molecule.
PCT/US2006/030245 2005-07-28 2006-07-28 Consecutive base single molecule sequencing Ceased WO2007014397A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP06800694A EP1907591A2 (en) 2005-07-28 2006-07-28 Consecutive base single molecule sequencing
CA002616433A CA2616433A1 (en) 2005-07-28 2006-07-28 Consecutive base single molecule sequencing

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US70377705P 2005-07-28 2005-07-28
US60/703,777 2005-07-28

Publications (2)

Publication Number Publication Date
WO2007014397A2 WO2007014397A2 (en) 2007-02-01
WO2007014397A3 true WO2007014397A3 (en) 2007-09-13

Family

ID=37307192

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2006/030245 Ceased WO2007014397A2 (en) 2005-07-28 2006-07-28 Consecutive base single molecule sequencing

Country Status (4)

Country Link
US (1) US20070099212A1 (en)
EP (1) EP1907591A2 (en)
CA (1) CA2616433A1 (en)
WO (1) WO2007014397A2 (en)

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9228228B2 (en) 2006-10-27 2016-01-05 Complete Genomics, Inc. Efficient arrays of amplified polynucleotides
US9238834B2 (en) 2007-11-29 2016-01-19 Complete Genomics, Inc. Efficient shotgun sequencing methods
US9334490B2 (en) 2006-11-09 2016-05-10 Complete Genomics, Inc. Methods and compositions for large-scale analysis of nucleic acids using DNA deletions
US9476054B2 (en) 2005-06-15 2016-10-25 Complete Genomics, Inc. Two-adaptor library for high-throughput sequencing on DNA arrays
US9499863B2 (en) 2007-12-05 2016-11-22 Complete Genomics, Inc. Reducing GC bias in DNA sequencing using nucleotide analogs

Families Citing this family (38)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998035012A2 (en) * 1997-02-12 1998-08-13 Chan Eugene Y Methods and products for analyzing polymers
WO2002044425A2 (en) * 2000-12-01 2002-06-06 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
CN103396933B (en) 2003-02-26 2016-04-20 凯利达基因组股份有限公司 By hybridizing the random array DNA analysis carried out
CN101466847B (en) 2005-06-15 2014-02-19 考利达基因组股份有限公司 Single-molecule arrays for genetic and chemical analysis
US7805081B2 (en) * 2005-08-11 2010-09-28 Pacific Biosciences Of California, Inc. Methods and systems for monitoring multiple optical signals from a single source
US20090305248A1 (en) * 2005-12-15 2009-12-10 Lander Eric G Methods for increasing accuracy of nucleic acid sequencing
US7715001B2 (en) * 2006-02-13 2010-05-11 Pacific Biosciences Of California, Inc. Methods and systems for simultaneous real-time monitoring of optical signals from multiple sources
US7692783B2 (en) * 2006-02-13 2010-04-06 Pacific Biosciences Of California Methods and systems for simultaneous real-time monitoring of optical signals from multiple sources
US7995202B2 (en) * 2006-02-13 2011-08-09 Pacific Biosciences Of California, Inc. Methods and systems for simultaneous real-time monitoring of optical signals from multiple sources
US8207509B2 (en) 2006-09-01 2012-06-26 Pacific Biosciences Of California, Inc. Substrates, systems and methods for analyzing materials
AU2007289057C1 (en) * 2006-09-01 2014-01-16 Pacific Biosciences Of California, Inc. Substrates, systems and methods for analyzing materials
US20080080059A1 (en) * 2006-09-28 2008-04-03 Pacific Biosciences Of California, Inc. Modular optical components and systems incorporating same
US20100167413A1 (en) * 2007-05-10 2010-07-01 Paul Lundquist Methods and systems for analyzing fluorescent materials with reduced autofluorescence
US20080277595A1 (en) * 2007-05-10 2008-11-13 Pacific Biosciences Of California, Inc. Highly multiplexed confocal detection systems and methods of using same
JP2011505119A (en) * 2007-10-22 2011-02-24 ライフ テクノロジーズ コーポレーション Method and system for obtaining ordered and fragmented sequence fragments along a nucleic acid molecule
US8415099B2 (en) 2007-11-05 2013-04-09 Complete Genomics, Inc. Efficient base determination in sequencing reactions
WO2009097368A2 (en) 2008-01-28 2009-08-06 Complete Genomics, Inc. Methods and compositions for efficient base calling in sequencing reactions
WO2009097626A2 (en) * 2008-02-03 2009-08-06 Helicos Biosciences Corporation Paired-end reads in sequencing by synthesis
WO2009120372A2 (en) 2008-03-28 2009-10-01 Pacific Biosciences Of California, Inc. Compositions and methods for nucleic acid sequencing
US20090247426A1 (en) * 2008-03-31 2009-10-01 Pacific Biosciences Of California, Inc. Focused library generation
US8795961B2 (en) * 2008-09-05 2014-08-05 Pacific Biosciences Of California, Inc. Preparations, compositions, and methods for nucleic acid sequencing
DK3629011T3 (en) * 2008-09-16 2024-01-29 Pacific Biosciences California Inc INTEGRATED OPTICAL DEVICE
US9524369B2 (en) 2009-06-15 2016-12-20 Complete Genomics, Inc. Processing and analysis of complex nucleic acid sequence data
WO2011017656A2 (en) * 2009-08-06 2011-02-10 Ibis Biosciences, Inc. Non-mass determined base compositions for nucleic acid detection
WO2011103507A1 (en) 2010-02-19 2011-08-25 Pacific Biosciences Of California, Inc. Optics collection and detection system and method
US8994946B2 (en) 2010-02-19 2015-03-31 Pacific Biosciences Of California, Inc. Integrated analytical system and method
US8993737B2 (en) 2010-08-25 2015-03-31 Pacific Biosciences, Inc. Phospholinked dye analogs with an amino acid linker
US9315864B2 (en) 2012-05-18 2016-04-19 Pacific Biosciences Of California, Inc. Heteroarylcyanine dyes with sulfonic acid substituents
WO2013173844A1 (en) 2012-05-18 2013-11-21 Pacific Biosciences Of California, Inc. Heteroarylcyanine dyes
US9372308B1 (en) 2012-06-17 2016-06-21 Pacific Biosciences Of California, Inc. Arrays of integrated analytical devices and methods for production
US9223084B2 (en) 2012-12-18 2015-12-29 Pacific Biosciences Of California, Inc. Illumination of optical analytical devices
US9624540B2 (en) 2013-02-22 2017-04-18 Pacific Biosciences Of California, Inc. Integrated illumination of optical analytical devices
CA2959518A1 (en) 2014-08-27 2016-03-03 Pacific Biosciences Of California, Inc. Arrays of integrated analytical devices
US10487356B2 (en) 2015-03-16 2019-11-26 Pacific Biosciences Of California, Inc. Integrated devices and systems for free-space optical coupling
EP3292220B1 (en) 2015-05-07 2022-07-13 Pacific Biosciences of California, Inc. Multiprocessor pipeline architecture
US10365434B2 (en) 2015-06-12 2019-07-30 Pacific Biosciences Of California, Inc. Integrated target waveguide devices and systems for optical coupling
US12535420B2 (en) 2020-02-18 2026-01-27 Pacific Biosciences Of California, Inc. Highly multiplexed nucleic acid sequencing systems
CN117642514A (en) 2021-05-04 2024-03-01 加利福尼亚太平洋生物科学股份有限公司 Arrays of Integrated Analytical Devices with Reduced Scale Cell Wells

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2005040425A2 (en) * 2003-10-20 2005-05-06 Isis Innovation Ltd Nucleic acid sequencing methods
US20050100932A1 (en) * 2003-11-12 2005-05-12 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
WO2005080605A2 (en) * 2004-02-19 2005-09-01 Helicos Biosciences Corporation Methods and kits for analyzing polynucleotide sequences

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6090593A (en) * 1998-05-13 2000-07-18 The United States Of America As Represented By The Secretary Of The Air Force Isolation of expressed genes in microorganisms
AU772281B2 (en) * 1998-12-14 2004-04-22 Li-Cor Inc. A system and methods for nucleic acid sequencing of single molecules by polymerase synthesis
US7056661B2 (en) * 1999-05-19 2006-06-06 Cornell Research Foundation, Inc. Method for sequencing nucleic acid molecules
EP1337541B1 (en) * 2000-10-06 2007-03-07 The Trustees of Columbia University in the City of New York Massive parallel method for decoding DNA and RNA
US20030232365A1 (en) * 2001-02-15 2003-12-18 Whitehead Institute For Biomedical Research BDNF polymorphisms and association with bipolar disorder

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2005040425A2 (en) * 2003-10-20 2005-05-06 Isis Innovation Ltd Nucleic acid sequencing methods
US20050100932A1 (en) * 2003-11-12 2005-05-12 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
WO2005047523A2 (en) * 2003-11-12 2005-05-26 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
WO2005080605A2 (en) * 2004-02-19 2005-09-01 Helicos Biosciences Corporation Methods and kits for analyzing polynucleotide sequences

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
BRASLAVSKY IDO ET AL: "Sequence information can be obtained from single DNA molecules", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE, WASHINGTON, DC, US, vol. 100, no. 7, 1 April 2003 (2003-04-01), pages 3960 - 3964, XP002341053, ISSN: 0027-8424 *
KARTALOV EMIL P ET AL: "Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 32, no. 9, 2004, pages 2873 - 2879, XP002341056, ISSN: 0305-1048 *
METZKER M L: "EMERGING TECHNOLOGIES IN DNA SEQUENCING", GENOME RESEARCH, COLD SPRING HARBOR LABORATORY PRESS, WOODBURY, NY, US, vol. 15, no. 12, December 2005 (2005-12-01), pages 1767 - 1776, XP002379405, ISSN: 1088-9051 *
SEO TAE SEOK ET AL: "Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE, WASHINGTON, DC, US, vol. 101, no. 15, 13 April 2004 (2004-04-13), pages 5488 - 5493, XP002341057, ISSN: 0027-8424 *

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9476054B2 (en) 2005-06-15 2016-10-25 Complete Genomics, Inc. Two-adaptor library for high-throughput sequencing on DNA arrays
US9228228B2 (en) 2006-10-27 2016-01-05 Complete Genomics, Inc. Efficient arrays of amplified polynucleotides
US9334490B2 (en) 2006-11-09 2016-05-10 Complete Genomics, Inc. Methods and compositions for large-scale analysis of nucleic acids using DNA deletions
US9238834B2 (en) 2007-11-29 2016-01-19 Complete Genomics, Inc. Efficient shotgun sequencing methods
US9499863B2 (en) 2007-12-05 2016-11-22 Complete Genomics, Inc. Reducing GC bias in DNA sequencing using nucleotide analogs

Also Published As

Publication number Publication date
CA2616433A1 (en) 2007-02-01
WO2007014397A2 (en) 2007-02-01
US20070099212A1 (en) 2007-05-03
EP1907591A2 (en) 2008-04-09

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